Figure 6. The binding models of Mnk inhibitors.
(A) Interactions of CGP57380 (green) within the ATP binding domain, and (B) schematic presentation of the corresponding interactions. (C) Interactions of cercosporamide (green) within the ATP binding domain, and (D) schematic presentation of the corresponding interactions. The DFD motif: pink sticks; Hinge region: orange sticks; Gate keeper: red sticks; Inhibitors: green sticks. Hydrogen bonds: dashed lines; Hydrophobic region I: shaded pink; Hydrophobic region II: shaded light blue; Allosteric pocket: shaded light beige. The likely binding posts were generated by Autodock 4.0 (http://w3.to/autodock). The structure of the Mnk2-KRD228G–Staurosporine complex (PDB2HW7) was used as the initial template. The dimensions of the active site box were chosen to be large enough to encompass the entire ATP binding pocket and allosteric site. Docking calculations were carried out using the Lamarckian genetic algorithm (LGA). A maximum number of 2,500,000 energy evaluations were used. Each docking experiment consisted of 100 independent runs.